Expression partitioning of quinoa CLC genes under distinct Na+/Cl− regimes reveals root-centered ionic remodeling

The chloride channel-like ( CLC ) family plays central roles in anion transport, vacuolar compartmentation, and ionic homeostasis in plants, but the quinoa CLC family has not yet been examined within an integrated framework linking family definition, structural divergence, expression responses, and physiological context. Using the quinoa QQ74_V2 genome, we defined eight high-confidence CqCLC members through a strict core-set strategy and integrated phylogenetic analysis, gene structure, conserved motifs, promoter cis-elements, chromosomal distribution, synteny, transcriptome profiling, qRT-PCR, and physiological analyses. Most CqCLC members retained the conserved structural framework typical of plant CLC proteins, but clear divergence was detected in structural features, promoter composition, predicted localization, and expression behavior, with CqCLC08 showing the strongest deviation. Transcriptome and independent qRT-PCR analyses showed nonuniform family-wide responses, with CqCLC expression patterns varying among treatments, tissues, and sampling times; roots showed the strongest early transcriptional responses. Phenotype, SPAD, leaf N content, antioxidant enzyme activities, and Na + , K + , and Ca 2+ distribution further indicated that the tested salt treatments represented physiologically distinct ionic contexts rather than a simple stress-intensity gradient. By integrating structural, transcriptional, and physiological evidence, CqCLC01, CqCLC04, CqCLC05 , and CqCLC08 were prioritized as the most informative candidates for downstream functional validation. These findings provide a focused framework for dissecting anion homeostasis and putative ion-transport specialization in quinoa under complex salt environments.